1U9Q

Crystal structure of cruzain bound to an alpha-ketoester


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62910.6-1M NaCitrate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.9636.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.72α = 90
b = 50.675β = 116.74
c = 45.576γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298IMAGE PLATERIGAKU RAXIS IIYale MSC mirrors2000-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU3001.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.340.820.0925.178267826
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.32.3788.20.2072.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTcruzipain coordinate set 1AIM, without inhibitor or water molecules2.340.827826745736393.320.136270.132240.21773RANDOM14.744
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.05-0.730.09-0.78
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.413
r_dihedral_angle_4_deg19.529
r_dihedral_angle_3_deg15.443
r_dihedral_angle_1_deg6.616
r_scangle_it4.223
r_scbond_it2.669
r_angle_refined_deg1.876
r_mcangle_it1.599
r_mcbond_it0.988
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg43.413
r_dihedral_angle_4_deg19.529
r_dihedral_angle_3_deg15.443
r_dihedral_angle_1_deg6.616
r_scangle_it4.223
r_scbond_it2.669
r_angle_refined_deg1.876
r_mcangle_it1.599
r_mcbond_it0.988
r_nbtor_refined0.314
r_nbd_refined0.276
r_symmetry_vdw_refined0.273
r_xyhbond_nbd_refined0.186
r_symmetry_hbond_refined0.177
r_chiral_restr0.109
r_bond_refined_d0.02
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1592
Nucleic Acid Atoms
Solvent Atoms104
Heterogen Atoms30

Software

Software
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
REFMACrefinement
X-PLORphasing